Link to this post | posted 14 Jul, 2019 21:22

scaruso

Hello, We would like to propose the addition of TerD or tellurium resistance protein, or the equivalent, to the approved function list. We believe pham 15777, which currently includes: Geostin gene 71 (39028 - 39609) FlowerPower gene 76 (39028 - 39609) Fabian_Draft gene 79 (39358 - 39939) Shows compelling evidence for the functional call. Examination of the protein sequence here: >Geostin gp71 MINLTKGSAPVTLSKAARMSVRITWPAATDYDAGAEILYKDGTTESIATFGARGVDAKLTSLTGKVRHNGDATRGAGTATETIDIDHDDEIVEIRPWAYSAQSNGTGSFRKYAVSMEVSNGTDTVKIDANNASNHDNVYTCVPAVLRFTGDGVQVEYAELYSDPRSEARPAFKKSGLLGKLKFTMDGPRNNYK By HHPred: https://toolkit.tuebingen.mpg.de/#/jobs/SEAGEOSTIN71 And by BlastP: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=JPXJD11B01R Shows high coverage and high confidence matches to the tellurium resistance protein TerD in multiple bacterial species. A brief literature search found that the gene has been found in phages infecting : Salmonella and Cronobacter spp.: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-481 and https://atrium.lib.uoguelph.ca/xmlui/handle/10214/7414, Pseudomona spp https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178739/, Clostridium spp. https://www.ncbi.nlm.nih.gov/pubmed/17322187, and Bacillus spp.: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178739/ The domain, as shown in Phamerator is also found by the CDD: https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?RID=JPXJCJHM01R Thanks, Steve Edited 14 Jul, 2019 21:23

Link to this post | posted 01 Jul, 2019 21:02

scaruso

OK, here's a dumb question. But I figure, someone needs to ask them. I have seen the "Number of Genes" field in Phagesdb where it is a total including tRNA genes and where it doesn't include tRNAs gene and, presumably reflects only protein coding genes. I would assume it is supposed to be the CDS number since at the input it says '# of ORFs' not genes, but the output says 'genes.' Can you clarify, so I know for sure? Thanks, Steve

Link to this post | posted 28 Jun, 2019 15:58

scaruso

Excellent, Question, though. I caught up on the meeting that I had to leave from yesterday and have a question that pertains to this. Perhaps the new version of the virtual machine could include some of these useful tools all put together? The new Starterator from Chris, a standalone Aragorn in case we loose it in the future (or it's down again, or until we can host it somewhere), the new version of the splitstree prep-program, and the newest version of the checker? I'd happily upgrade. Steve

Link to this post | posted 25 Jun, 2019 15:41
scaruso	It won't load for me at all, still. I asked some people to try it at the last SMART meeting, and it didn't load for them either, so there may be something going on. Welkin mentioned she heard there may be a retirement coming up. Steve

Link to this post | posted 19 Jun, 2019 13:32
scaruso	Has anyone been having trouble accessing Aragorn? We have not been able to access it for a couple days now. Steve

Link to this post | posted 24 May, 2019 21:16
scaruso	These are big phages. S.

Link to this post | posted 24 May, 2019 21:12
scaruso	Ah. Thanks. That helps. Steve Edited 24 May, 2019 21:13

Link to this post | posted 24 May, 2019 18:04

scaruso

I am checking a BE1 submission, which have 40+ tRNAs. I noticed, as I go though them that I would not have accepted all of these. I've already found four with acceptor stems of 5 bp, 6 bp, and 8 bp, and a couple with very low scores (10 and 14), but that are present in other BE1 phages. Before I deleted them, I wanted to make sure there was no reason these were in there outside the guidlines. Thanks! Steve Edited 24 May, 2019 18:08

Link to this post | posted 20 May, 2019 21:13

scaruso

We certainly had problems with smears in the past. Most of the time, I have attributed it to user error, and we have switched to adding EDTA and proteinase K to our protocol. It has nearly, but not completely eliminated the issue. I think the few that remain are a mixture mostly of students that are incautious, and a few that are something else. We have phages that simply refuse to give us pretty DNA (the Bacillus phi29-like podos are a reliable example) unless we use phenol chloroform despite very high titers. That's consistent over several years among many students. We have to wonder if there is something interesting going on with their DNA or capsid, or a packaged enzyme that is being denatured by the phenol but not by the standard isolation. Then, this year, we had several, five I think, Streptomyces phages that were not cut at all when tested by every enzyme I could get my hands on (I think I had ten or so). These were enzymes that were consistently cutting other phages' DNA, so we knew they worked. So, not a smear, but modified DNA? Seems like a possibility. Steve

Link to this post | posted 16 May, 2019 18:56
scaruso	OK, so, after further consideration and looking at the second one, I think calling the first gene Lysin A is probably pretty safe. I don't know about calling the second one anything beyond hydrolase. Steve